Nanomaterials for Application in Medicine and Biology NATO Science for Peace and Security Series This Series presents the results of scientifi c meetings supported under the NATO Programme: Science for Peace and Security (SPS). The NATO SPS Programme supports meetings in the following Key Priority areas: (1) Defence Against Terrorism; (2) Countering other Threats to Security and (3) NATO, Partner and Mediter- ranean Dialogue Country Priorities. The types of meeting supported are generally "Advanced Study Institutes" and "Advanced Research Workshops". The NATO SPS Series collects together the results of these meetings. The meetings are coorganized by scientists from NATO countries and scientists from NATO's "Partner" or "Mediterranean Dialogue" countries. The observations and recommendations made at the meetings, as well as the contents of the volumes in the Series, refl ect those of participants and contributors only; they should not necessarily be regarded as refl ecting NATO views or policy. Advanced Study Institutes (ASI) are high-level tutorial courses intended to convey the latest developments in a subject to an advanced-level audience Advanced Research Workshops (ARW) are expert meetings where an intense but informal exchange of views at the frontiers of a subject aims at identifying directions for future action Following a transformation of the programme in 2006 the Series has been re-named and re-organised. Recent volumes on topics not related to security, which result from meetings supported under the programme earlier, may be found in the NATO Science Series. The Series is published by IOS Press, Amsterdam, and Springer, Dordrecht, in conjunction with the NATO Public Diplomacy Division. Sub-Series A. Chemistry and Biology Springer B. Physics and Biophysics Springer C. Environmental Security Springer D. Information and Communication Security IOS Press E. Human and Societal Dynamics IOS Press http://www.nato.int/science http://www.springer.com http://www.iospress.nl Series B: Physics and Biophysics Nanomaterials for Application in Medicine and Biology edited by Michael Giersig center of advanced european studies and research (caesar) Bonn, Germany and Gennady B. Khomutov Moscow State University Moscow, Russia Proceedings of the NATO Advanced Research Workshop on Nanomaterials for Application in Medicine and Biology Bonn, Germany 4–6 October 2006 A C.I.P. Catalogue record for this book is available from the Library of Congress. ISBN 978-1-4020-6828-7 (PB) ISBN 978-1-4020-6827-0 (HB) ISBN 978-1-4020-6829-4 (e-book) Published by Springer, P.O. Box 17, 3300 AA Dordrecht, The Netherlands. www.springer.com Printed on acid-free paper All Rights Reserved © 2008 Springer Science + Business Media B.V. No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form-or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. CONTENTS Preface vii Contributors ix 1. Biocompatible Nanomaterials and Nanodevices Promising for Biomedical Applications 1 I. Firkowska, S. Giannona, J. A. Rojas-Chapana, K. Luecke, O. Brüstle, and M. Giersig 2. Isohelical DNA-Binding Oligomers: Antiviral Activity and Application for the Design of Nanostructured Devices 17 G. Gursky, A. Nikitin, A. Surovaya, S. Grokhovsky, V. Andronova, and G. Galegov 3. DNA Self-Assembling Nanostructures Induced by Trivalent Ions and Polycations 29 N. Kasyanenko and D. Afanasieva 4. DNA-Based Synthesis and Assembly of Organized Iron Oxide Nanostructures 39 G. B. Khomutov 5. DNA-Based Nanostructures: Changes of Mechanical Properties of DNA upon Ligand Binding 59 Y. Nechipurenko, S. Grokhovsky, G. Gursky, D. Nechipurenko, and R. Polozov 6. Nanoconstructions Based on Spatially Ordered Nucleic Acid Molecules 69 Yu. M. Yevdokimov 7. Nanospearing – Biomolecule Delivery and Its Biocompatibility 81 D. Cai, K. Kempa, Z. Ren, D. Carnahan, and T. C. Chiles 8. Multifunctional Glyconanoparticles: Applications in Biology and Biomedicine 93 S. Penadés, J. M. de la Fuente, Á. G. Barrientos, C. Clavel, O. Martínez-Ávila, and D. Alcántara v 9. Plasmonics of Gold Nanorods. Considerations for Biosensing 103 L. M. Liz-Marzán, J. Pérez-Juste, and I. Pastoriza-Santos 10. Influence of the S-Au Bond Strength on the Magnetic Behavior of S-Capped Au Nanoparticles 113 M. J. Rodríguez Vázquez, J. Rivas, M. A. López-Quintela, A. Mouriño Mosquera, and M. Torneiro 11. Long-Term Retention of Fluorescent Quantum Dots In Vivo 127 B. Ballou, L. A. Ernst, S. Andreko, M. P. Bruchez, B. C. Lagerholm, and A. S. Waggoner 12. Towards Polymer-Based Capsules with Drastically Reduced Controlled Permeability 139 D. V. Andreeva and G. B. Sukhorukov 13. Polyelectrolyte-Mediated Transport of Doxorubicin Through the Bilayer Lipid Membrane 149 A. A. Yaroslavov, M. V. Kitaeva, N. S. Melik-Nubarov, and F. M. Menger 14. Network Model of Acetobacter Xylinum Cellulose Intercalated by Drug Nanoparticles 165 V. V. Klechkovskaya, V. V. Volkov, E. V. Shtykova, N. A. Arkharova, Y. G. Baklagina, A. K. Khripunov, R. Yu. Smyslov, L. N. Borovikova, and A. A. Tkachenko 15. Theoretical Approaches to Nanoparticles 179 K. Kempa vi Contents PREFACE This volume contains research reports presented during the NATO Advanced Research Workshop (ARW) “Materials for Application in Medicine and Biology” held in Bonn, Germany, from October 4 to 6, 2006 at the center of advanced european studies and research (caesar). The application of nanomaterials in medicine and biology can be understood as the gathering and use of our current knowledge on nanoscale features of bio- logical systems in order to learn how to design nanodevices for biomedical uses. The success of this approach, known as nano-engineering, will allow scientists to devise strategies for the design and construction of nanodevices to be used in clinical trials (diagnosis and therapeutic monitoring), as well as to develop products with potential applications in regenerative medicine. One goal of this conference was to bring together researchers from Eastern and Western countries, offering them a platform to meet and discuss results of their research work. Thus, the aim of this conference was not only to present the advancements in research achieved during the past years, but it had also been conceived as a concerted European effort where expertise, technologies, and ideas were broadly shared to accelerate this progress. The conference provided an interactive forum with more than 100 participants from 15 countries. The 15 selected papers cover the following topics: (1) nanodevices for biomedical applications; (2) DNA-nanoparticle conjugates; (3) transmem- brane delivery of macromolecules by nanomaterials and/or polyelectrolytes; (4) glyconanoparticles for biomedical purposes; (5) optical properties of gold nanoparticles and biosensing; (6) magnetic behavior of S-capped gold nano- particles; (7) quantum dots for biological tagging; (8) polymer-based cap- sules; (9) theoretical approaches to nanoparticles. The conference was organized by the Department of Nanoparticle Technology at the center of advanced european studies and research (caesar), with Professor Dr. Giersig as head-organizer, and Professor Dr. Khomutov from Moscow State University as co-organizer, in full cooperation with caesar, and generous financial support by NATO. We would especially like to thank the NATO Science Programme for providing a generous grant for the realization of this conference. We would also like to acknowledge and thank all those who participated in this event including those who provided expertise through the presentation of their research as well as everyone who engaged in discussions and contributed to the organization and planning of the conference – in short, all who helped to make the NATO Advanced Research Workshop 2006 a success. vii CONTRIBUTORS Daria Afanasieva Dept. of Molecular Biophysics, Faculty of Physics, St. Petersburg State University, Uluanovskaya St. 1, Petrodvorets, St. Petersburg, 198504, Russia David Alcántara Laboratory of Glyconanotechnology, CIC biomaGUNE and CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Paseo Miramón 182, Parque Tecnológico de San Sebastián, 20009 San Sebastián, Spain Daria V. Andreeva Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Golm/Potsdam, Germany Susan Andreko Molecular Biosensor and Imaging Center, Mellon Institute, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA Valeria Andronova D.I. Ivanovsky Institute of Virology, Russian Academy of Medical Sciences, Gamaleya Str. 16, Moscow, 123098, Russia Natalia A. Arkharova Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, Moscow, 119333, Russia Yulia G. Baklagina Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi pr. 31, St. Petersburg, 199004, Russia Byron Ballou Molecular Biosensor and Imaging Center/Department of Biological Sciences, Mellon Institute, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA ix África G. Barrientos Laboratory of Glyconanotechnology, CIC biomaGUNE and CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Paseo Miramón 182, Parque Tecnológico de San Sebastián, 20009 San Sebastián, Spain Ludmila N. Borovikova Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi pr. 31, St. Petersburg, 199004, Russia Marcel P. Bruchez Molecular Biosensor and Imaging Center/Department of Chemistry, Mellon Institute, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA Oliver Brüstle Institute of Reconstructive Neurobiology, Life and Brain Center, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany Dong Cai Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA/NanoLab, Inc., Newton, MA 02458, USA David Carnahan NanoLab, Inc., Newton, MA 02458, USA Thomas C. Chiles Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA Caroline Clavel Laboratory of Glyconanotechnology, CIC biomaGUNE and CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Paseo Miramón 182, Parque Tecnológico de San Sebastián, 20009 San Sebastián, Spain Lauren A. Ernst Molecular Biosensor and Imaging Center, Mellon Institute, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA x Contributors Izabela Firkowska center of advanced european studies and research (caesar), Nanoparticle Technology Dept., Ludwig-Erhard-Allee 2, 53175 Bonn, Germany Jesus M. de la Fuente Laboratory of Glyconanotechnology, CIC biomaGUNE and CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Paseo Miramón 182, Parque Tecnológico de San Sebastián, 20009 San Sebastián, Spain Georgy Galegov D.I. Ivanovsky Institute of Virology, Russian Academy of Medical Sciences, Gamaleya Str. 16, Moscow, 123098, Russia Suna Giannona center of advanced european studies and research (caesar), Nanoparticle Technology Dept., Ludwig-Erhard-Allee 2, 53175 Bonn, Germany Michael Giersig center of advanced european studies and research (caesar), Nanoparticle Technology Dept., Ludwig-Erhard-Allee 2, 53175 Bonn, Germany Sergey Grokhovsky V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow, 119991, Russia Georgy Gursky V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow, 119991, Russia Nina Kasyanenko Dept. of Molecular Biophysics, Faculty of Physics, St. Petersburg State University, Uluanovskaya St. 1, Petrodvorets, St. Petersburg, 198504, Russia Krzysztof Kempa Department of Physics, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA Contributors xi [...]... netropsin and distamycin A (for a review, see Bailly and Chaires1) X-ray2–4 and NMR5 studies show that these two antibiotics bind in the minor DNA groove at runs of four or five AT-base pairs Their binding specificity derives from specific hydrogen-bonding interactions between the amide NH groups of the antibiotic molecule and the thymine O2 and adenine N3 atoms, van-der-Waals forces, and electrostatic interactions... method in its application to bio-sensing is the high-throughput sensing and the potential of simultaneously monitoring many targets in one substrate, which is essential in biosensing technology In addition, being bound to a substrate (wafer) greatly increases the efficacy of these nanoislands for use in bio-sensing applications However, the efficacy of the nano-islands as nanosensors is strongly influenced... phenomena encountered in biological systems The results emerging from these studies create an exciting focus for research in the bioengineering field On the other hand, recent results obtained on nanosensory include the development of biosensing-chips for the recognition, trapping, and immobilization of rare cells types in peripheral blood The biosensing-chip relies on gold nano-islands combined with an antigen-antibody... showing an array of aligned carbon nanotubes intended for delivering foreign material into cells quickly and efficiently In this case, the nanotubes will leave the cells clean and unharmed Nanomaterials for Biomedicine 5 Taking into account that carbon nanotubes are hollow cylinders, they can store active substances, thus the same nano-electroporative approach may be used for localized drug delivery In. .. we modified the structure of known DNA-binding compounds and constructed new compounds from fragments of DNA-binding antibiotics and dyes directly in the minor DNA groove Ligands that could serve as DNA binders were inserted into the minor DNA groove and optimization in the MMFF9431 as well as in Florent’ev’s molecular-mechanical force fields was carried out and we found a number of new structural... hydrogen bonding is observed for N-methyl hydroxypyrrole residues incorporated in motif I.34 On the basis of motifs I and V, we constructed a DNA-binding ligand in which two netropsin fragments (motif I) are covalently linked via the pseudopeptide containing glycine, 5-aminomethylfuran-2-carboxylic acid and malonic acid residues (Fig 5) As revealed by CD spectroscopy studies, the bis-linked netropsin derivative... some of these compounds exhibit a high binding specificity and selectively inhibit initiation of transcription directed by certain procaryotic and eukaryotic promoters.7,25 Bis-linked netropsin derivatives inhibit the activity of topoisomerases I and II,16,17 HIV-1 reverse transcriptase18 and integrase.19 It is also shown that bis-netropsins containing a two-stranded antiparallel peptide motif can recognize... containing six repeating units occupies twelve DNA base pairs upon binding In the complex, the nitrogen of the thiazole ring and the carbonyl oxygen of glycine in each repeating unit are hydrogen-bonded to the guanine 2-amino groups of two successive GC-pairs Replacement of thiazole by N-methyl hydroxypyrrole leads to a sterical clash caused by repulsive interaction between the guanine 2-amino group and. .. AT- and GC-base pairs.13 NMR and x-ray studies showed that two distamycin (lexitropsin) molecules can be packed in an antiparallel side-by-side manner in the minor DNA groove.2,10,15 The side-by-side dimer motif was used by Dervan and coworkers for the design of covalently linked polyamide dimers containing N-methylpyrrole- and N-methylimidazole-carboxamide units.11,14 These ligands in hairpin form... Khomutov (eds.), Nanomaterials for Application in Medicine and Biology © Springer Science + Business Media B.V 2008 1 2 I Firkowska et al Novel materials engineered at the nanometer scale (nanomaterials) are indispensable elements on the whole field of nanotechnology They can be considered as the most important crossing between basic research and marketable products and processes Nanomaterials show . Giersig and G. B. Khomutov (eds.), 1 Nanomaterials for Application in Medicine and Biology © Springer Science + Business Media B.V. 2008 Biocompatible Nanomaterials and Nanodevices Promising for. Press http://www.nato.int/science http://www.springer.com http://www.iospress.nl Series B: Physics and Biophysics Nanomaterials for Application in Medicine and Biology edited by Michael Giersig center of advanced european. Nanomaterials for Application in Medicine and Biology NATO Science for Peace and Security Series This Series presents the results of scientifi c meetings supported under the NATO Programme: